Related papers: Exploring DNA translocation through a nanopore via…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Nanoporous capsules have been the subject of intense investigation in the field of drug delivery. One of the essential properties of such particles, which requires characterization, is their structure. Many experimental techniques have been…
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule…
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of…
Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
The fluidic behavior of water at the micro/nano scale is studied by using of single DNA molecules as a model system. Stable curved DNA patterns with spans about one micron were generated by using of water flows, and observed by Atomic Force…
Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have…
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA…
Particles with ligand-receptor contacts bind and unbind fluctuating "legs" to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such "nanoscale caterpillars" is a challenge, since binding events often…
We investigate the translocation of a single stranded DNA (ssDNA) through a pore, which fluctuates between two conformations, by using coupled master equations (ME). The probability density function (PDF) of the first passage times (FPT) of…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore and…
Electrokinetic transport phenomena can strongly influence the behaviour of macromolecules and colloidal particles in solution, with applications in, e.g., DNA translocation through nanopores, electro-osmotic flow in nanocapillaries, and…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…